X core promoter element gene transcriptions: Difference between revisions

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==XCPE1 random dataset samplings==
==XCPE1 random dataset samplings==


# RDr0: 0.
# XCPE1r0: 0.
# RDr1: 0.
# RDr1: 0.
# RDr2: 0.
# RDr2: 0.

Revision as of 21:10, 20 March 2023

Editor-In-Chief: Henry A. Hoff

File:2013 E3 Snail USA Photo Op.jpg
The image shows a group of people gathered to promote a computer game. Credit: - EMR -.

The core promoter element X core promoter element 1 (XCPE1) directs activator-, mediator-, protein-dependent but TFIID-independent RNA polymerase II transcription from TATA box-less promoters.[1]

This promoter element appears to be exclusively human such as the group in the image at the right.

Consensus sequences

Main article: Consensus sequence gene transcriptions

"[T]he X gene core promoter element 1 ... is located between nucleotides -8 and +2 relative to the transcriptional start site (+1) and has a consensus sequence of G/A/T-G/C-G-T/C-G-G-G/A-A-G/C+1-A/C."[1]

Gene expressions

Main article: Gene expressions

Although it is harder to regulate the transcription of genes with multiple transcription start sites, "variations in the expression of a constitutive gene would be minimized by the use of multiple start sites."[2]

Human genes

Main article: Human genes

"XCPE1 is ... found in the core promoter regions of about 1% of human genes, particularly in poorly characterized TATA-less genes."[1]

Gene transcriptions

Main article: Gene transcriptions

"From a teleological standpoint, this arrangement [of focused promoters] is consistent with the notion that it would be easier to regulate the transcription of a gene with a single transcription start site than one with multiple start sites."[2]

Focused promoters

Main article: Focused promoter gene transcriptions

"In focused transcription, there is either a single major transcription start site or several start sites within a narrow region of several nucleotides. Focused transcription is the predominant mode of transcription in simpler organisms."[2]

"Focused transcription initiation occurs in all organisms, and appears to be the predominant or exclusive mode of transcription in simpler organisms."[2]

"In vertebrates, focused transcription tends to be associated with regulated promoters".[2]

"The analysis of focused core promoters has led to the discovery of sequence motifs such as the TATA box, BREu (upstream TFIIBrecognition element), Inr (initiator), MTE (motif ten element), DPE (downstream promoter element), DCE (downstream core element), and XCPE1 (Xcore promoter element 1) [...]."[2]

Dispersed promoters

Main article: Dispersed promoter gene transcriptions

"In dispersed transcription, there are several weak transcription start sites over a broad region of about 50 to 100 nucleotides. Dispersed transcription is the most common mode of transcription in vertebrates. For instance, dispersed transcription is observed in about two-thirds of human genes."[2]

In vertebrates, "dispersed transcription is typically observed in constitutive promoters in CpG islands."[2]

Core promoters

Main article: Core promoter gene transcriptions

"Focused transcription typically initiates within the Inr, and the A nucleotide in the Inr consensus is usually designed as the “+ 1” position, whether or not transcription actually initiates at that particular nucleotide. This convention is useful because other core promoter motifs, such as the MTE and DPE, function with the Inr in a manner that exhibits a strict spacing dependence with the Inr consensus sequence (and hence, the A + 1 nucleotide) rather than the actual transcription start site (Burke and Kadonaga, 1997, Kutach and Kadonaga, 2000 and Lim et al., 2004)."[2]

"NC2 (negative cofactor 2; also known as Dr1-Drap1) [...] was identified as repressor of TATA-dependent transcription [...]."[2]

"Several core promoter elements have been previously identified in eukaryotes, but those cannot account for transcription from most RNA polymerase II-transcribed genes."[1]

XCPE1 samplings

For the Basic programs (starting with SuccessablesXCPE1.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:

  1. negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesXCPE1--.bas, looking for 3'-G/A/T-G/C-G-T/C-G-G-G/A-A-G/C-A/C-5', 1, 3'-TGGTGGGACC-5', 3744,
  2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesXCPE1-+.bas, looking for 3'-G/A/T-G/C-G-T/C-G-G-G/A-A-G/C-A/C-5', 0,
  3. positive strand in the negative direction is SuccessablesXCPE1+-.bas, looking for 3'-G/A/T-G/C-G-T/C-G-G-G/A-A-G/C-A/C-5', 0,
  4. positive strand in the positive direction is SuccessablesXCPE1++.bas, looking for 5'-(A/G/T)(C/G)G(C/T)GG(A/G)A(C/G)(A/C)-3', 1, 5'-GGGTGGAAGC-3' at 1406,
  5. complement, negative strand, negative direction is SuccessablesXCPE1c--.bas, looking for 3'-C/A/T-G/C-C-A/G-C-C-C/T-T-G/C-G/T-5', 0,
  6. complement, negative strand, positive direction is SuccessablesXCPE1c-+.bas, looking for 3'-C/A/T-G/C-C-A/G-C-C-C/T-T-G/C-G/T-5', 1, 5'-CCCACCTTCG-3' at 1406,
  7. complement, positive strand, negative direction is SuccessablesXCPE1c+-.bas, looking for 3'-C/A/T-G/C-C-A/G-C-C-C/T-T-G/C-G/T-5', 1, 3'-ACCACCCTGG-5', 3744,
  8. complement, positive strand, positive direction is SuccessablesXCPE1c++.bas, looking for 3'-C/A/T-G/C-C-A/G-C-C-C/T-T-G/C-G/T-5', 0,
  9. inverse complement, negative strand, negative direction is SuccessablesXCPE1ci--.bas, looking for 3'-G/T-G/C-T-C/T-C-C-A/G-C-G/C-C/A/T-5', 0,
  10. inverse complement, negative strand, positive direction is SuccessablesXCPE1ci-+.bas, looking for 3'-G/T-G/C-T-C/T-C-C-A/G-C-G/C-C/A/T-5', 0,
  11. inverse complement, positive strand, negative direction is SuccessablesXCPE1ci+-.bas, looking for 3'-G/T-G/C-T-C/T-C-C-A/G-C-G/C-C/A/T-5', 1, 5'-GCTCCCACCT-3' at 392, and complement.
  12. inverse complement, positive strand, positive direction is SuccessablesXCPE1ci++.bas, looking for 3'-G/T-G/C-T-C/T-C-C-A/G-C-G/C-C/A/T-5', 2, 5'-GGTCCCACCC-3' at 3541, 5'-TCTCCCACCT-3' at 185, and complements.
  13. inverse, negative strand, negative direction, is SuccessablesXCPE1i--.bas, looking for 3'-A/C-G/C-A-G/A-G-G-T/C-G-G/C-G/A/T-5', 1, 3'-CGAGGGTGGA-5', 392,
  14. inverse, negative strand, positive direction, is SuccessablesXCPE1i-+.bas, looking for 3'-A/C-G/C-A-G/A-G-G-T/C-G-G/C-G/A/T-5', 2, 5'-CCAGGGTGGG-3' at 3541, 5'-AGAGGGTGGA-3' at 185,
  15. inverse, positive strand, negative direction, is SuccessablesXCPE1i+-.bas, looking for 3'-A/C-G/C-A-G/A-G-G-T/C-G-G/C-G/A/T-5', 0,
  16. inverse, positive strand, positive direction, is SuccessablesXCPE1i++.bas, looking for 3'-A/C-G/C-A-G/A-G-G-T/C-G-G/C-G/A/T-5', 0.

XCPE1 (4560-2846) UTRs

  1. Negative strand, negative direction: TGGTGGGACC at 3744.

XCPE1 negative direction (2596-1) distal promoters

  1. Positive strand, negative direction: GCTCCCACCT at 392.

XCPE1 positive direction (4050-1) distal promoters

  1. Positive strand, positive direction: GGGTGGAAGC at 1406.
  2. Positive strand, positive direction: GGTCCCACCC at 3541, TCTCCCACCT at 185.

XCPE1 random dataset samplings

  1. XCPE1r0: 0.
  2. RDr1: 0.
  3. RDr2: 0.
  4. RDr3: 0.
  5. RDr4: 0.
  6. RDr5: 0.
  7. RDr6: 0.
  8. RDr7: 0.
  9. RDr8: 0.
  10. RDr9: 0.
  11. RDr0ci: 0.
  12. RDr1ci: 0.
  13. RDr2ci: 0.
  14. RDr3ci: 0.
  15. RDr4ci: 0.
  16. RDr5ci: 0.
  17. RDr6ci: 0.
  18. RDr7ci: 0.
  19. RDr8ci: 0.
  20. RDr9ci: 0.

RDr arbitrary (evens) (4560-2846) UTRs

RDr alternate (odds) (4560-2846) UTRs

RDr arbitrary negative direction (evens) (2846-2811) core promoters

RDr alternate negative direction (odds) (2846-2811) core promoters

RDr arbitrary positive direction (odds) (4445-4265) core promoters

RDr alternate positive direction (evens) (4445-4265) core promoters

RDr arbitrary negative direction (evens) (2811-2596) proximal promoters

RDr alternate negative direction (odds) (2811-2596) proximal promoters

RDr arbitrary positive direction (odds) (4265-4050) proximal promoters

RDr alternate positive direction (evens) (4265-4050) proximal promoters

RDr arbitrary negative direction (evens) (2596-1) distal promoters

RDr alternate negative direction (odds) (2596-1) distal promoters

RDr arbitrary positive direction (odds) (4050-1) distal promoters

RDr alternate positive direction (evens) (4050-1) distal promoters

XCPE1 analysis and results

Main article: Complex locus A1BG and ZNF497 § XCPE1s

"[T]he X gene core promoter element 1 ... has a consensus sequence of G/A/T-G/C-G-T/C-G-G-G/A-A-G/C+1-A/C."[1]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 1 2 0.5 0.5
Randoms UTR arbitrary negative 0 10 0 0
Randoms UTR alternate negative 0 10 0 0
Reals Core negative 0 2 0 0
Randoms Core arbitrary negative 0 10 0 0
Randoms Core alternate negative 0 10 0 0
Reals Core positive 0 2 0 0
Randoms Core arbitrary positive 0 10 0 0
Randoms Core alternate positive 0 10 0 0
Reals Proximal negative 0 2 0 0
Randoms Proximal arbitrary negative 0 10 0 0
Randoms Proximal alternate negative 0 10 0 0
Reals Proximal positive 0 2 0 0
Randoms Proximal arbitrary positive 0 10 0 0
Randoms Proximal alternate positive 0 10 0 0
Reals Distal negative 1 2 0.5 0.5
Randoms Distal arbitrary negative 0 10 0 0
Randoms Distal alternate negative 0 10 0 0
Reals Distal positive 3 2 1.5 1.5 ± 0.5 (-+0,++2)
Randoms Distal arbitrary positive 0 10 0 0
Randoms Distal alternate positive 0 10 0 0

Comparison:

The occurrences of real XCPE1s are greater than the randoms. This suggests that the real XCPE1s are likely active or activable.

Hypotheses

Main article: Hypotheses
  1. XCPE1 does not participate in the transcription of A1BG.

See also

References

  1. ↑ 1.0 1.1 1.2 1.3 1.4 Yumiko Tokusumi, Ying Ma, Xianzhou Song, Raymond H. Jacobson, and Shinako Takada (March 2007). "The New Core Promoter Element XCPE1 (X Core Promoter Element 1) Directs Activator-, Mediator-, and TATA-Binding Protein-Dependent but TFIID-Independent RNA Polymerase II Transcription from TATA-Less Promoters". Molecular and Cellular Biology. 27 (5): 1844–58. doi:10.1128/MCB.01363-06. PMID 17210644. Retrieved 2013-02-09.
  2. ↑ 2.0 2.1 2.2 2.3 2.4 2.5 2.6 2.7 2.8 2.9 Tamar Juven-Gershon and James T. Kadonaga (15 March 2010). "Regulation of gene expression via the core promoter and the basal transcriptional machinery". Developmental Biology. 339 (2): 225–9. doi:10.1016/j.ydbio.2009.08.009. Retrieved 2016-01-16.

Further reading

External links

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